def test_get_cds_codons_file(tmp_file):
"""
Test :py:func:`riboviz.get_cds_codons.get_cds_codons_file` with
FASTA file (:py:const:`TEST_FASTA_CODONS_FILE`) and GFF file
(:py:const:`TEST_GFF_CODONS_FILE`) and validate the TSV file output.
:param tmp_file: Temporary file
:type tmp_file: str or unicode
"""
get_cds_codons.get_cds_codons_file(TEST_FASTA_CODONS_FILE,
TEST_GFF_CODONS_FILE, tmp_file)
check_feature_codons_csv(TEST_CDS_CODONS, tmp_file)
def test_get_cds_codons_file_empty_gff_file(tmp_file):
"""
Test :py:func:`riboviz.get_cds_codons.get_cds_codons_file` with
FASTA file (:py:const:`TEST_FASTA_CODONS_FILE`) and an
empty GFF file raises an exception.
:param tmp_file: Temporary file
:type tmp_file: str or unicode
"""
with pytest.raises(ValueError):
get_cds_codons.get_cds_codons_file(TEST_FASTA_CODONS_FILE, tmp_file,
tmp_file)
def test_get_cds_codons_file_empty_fasta_file(tmp_file):
"""
Test :py:func:`riboviz.get_cds_codons.get_cds_codons_file` with an empty
FASTA file and GFF file (:py:const:`TEST_GFF_CODONS_FILE`) raises
an exception.
:param tmp_file: Temporary file
:type tmp_file: str or unicode
"""
with pytest.raises(FastaIndexingError):
get_cds_codons.get_cds_codons_file(tmp_file, TEST_GFF_CODONS_FILE,
tmp_file)
def test_get_cds_codons_file_no_such_fasta_file(tmp_file):
"""
Test :py:func:`riboviz.get_cds_codons.get_cds_codons_file` with a
non-existent FASTA file and GFF file
(:py:const:`TEST_GFF_CODONS_FILE`) raises an exception.
:param tmp_file: Temporary file
:type tmp_file: str or unicode
"""
with pytest.raises(FileNotFoundError):
get_cds_codons.get_cds_codons_file("nosuch.fasta",
TEST_GFF_CODONS_FILE, tmp_file)
def test_get_cds_codons_file_exclude_stop_codons(tmp_file):
"""
Test :py:func:`riboviz.get_cds_codons.get_cds_codons_file` with
FASTA file (:py:const:`TEST_FASTA_CODONS_FILE`) and GFF file
(:py:const:`TEST_GFF_CODONS_FILE`), where stop codons are to be
be excluded from the codons returned, and validate the TSV file
output.
:param tmp_file: Temporary file
:type tmp_file: str or unicode
"""
get_cds_codons.get_cds_codons_file(TEST_FASTA_CODONS_FILE,
TEST_GFF_CODONS_FILE,
tmp_file,
exclude_stop_codons=True)
cds_codons_minus_stops = {
name: codons[:-1]
for name, codons in TEST_CDS_CODONS.items()
}
check_feature_codons_csv(cds_codons_minus_stops, tmp_file)
def test_get_cds_codons_file_use_feature_name_true(tmp_file):
"""
Test :py:func:`riboviz.get_cds_codons.get_cds_codons_file` with
FASTA file (:py:const:`TEST_FASTA_CODONS_FILE`) and GFF file
(:py:const:`TEST_GFF_CODONS_FILE`) and ``use_feature_name=True``
and validate the TSV file output.
:param tmp_file: Temporary file
:type tmp_file: str or unicode
"""
get_cds_codons.get_cds_codons_file(TEST_FASTA_CODONS_FILE,
TEST_GFF_CODONS_FILE,
tmp_file,
use_feature_name=True)
# Update TEST_CDS_CODONS with the expected result when
# use_feature_name=True.
test_cds_codons = TEST_CDS_CODONS.copy()
codons = test_cds_codons[TEST_ID_NAME_ATTR_ID]
del test_cds_codons[TEST_ID_NAME_ATTR_ID]
test_cds_codons[TEST_ID_NAME_ATTR_NAME] = codons
check_feature_codons_csv(test_cds_codons, tmp_file)
def test_get_cds_codons_file_cds_format(tmp_file):
"""
Test :py:func:`riboviz.get_cds_codons.get_cds_codons_file` with
FASTA file (:py:const:`TEST_FASTA_CODONS_FILE`) and GFF file
(:py:const:`TEST_GFF_CODONS_FILE`) and custom
``cds_feature_format`` and validate the TSV file output.
:param tmp_file: Temporary file
:type tmp_file: str or unicode
"""
cds_feature_format = "{}-Custom"
get_cds_codons.get_cds_codons_file(TEST_FASTA_CODONS_FILE,
TEST_GFF_CODONS_FILE,
tmp_file,
cds_feature_format=cds_feature_format)
# Create expected results for custom cds_feature_format.
test_cds_codons = TEST_CDS_CODONS.copy()
codons = test_cds_codons[TEST_NO_ID_NAME_ATTR]
del test_cds_codons[TEST_NO_ID_NAME_ATTR]
test_cds_codons[cds_feature_format.format(
TEST_NO_ID_NAME_ATTR_PREFIX)] = codons
check_feature_codons_csv(test_cds_codons, tmp_file)
def invoke_get_cds_codons():
"""
Parse command-line options then invoke
:py:func:`riboviz.get_cds_codons.get_cds_codons_file`.
"""
print(provenance.write_provenance_to_str(__file__))
options = parse_command_line_options()
fasta = options.fasta
gff = options.gff
cds_codons = options.cds_codons
exclude_stop_codons = options.exclude_stop_codons
cds_feature_format = options.cds_feature_format
use_feature_name = options.use_feature_name
try:
get_cds_codons.get_cds_codons_file(fasta, gff, cds_codons,
exclude_stop_codons,
cds_feature_format,
use_feature_name)
except FastaIndexingError as e:
print("{}: {}".format(type(e).__name__, e))
except FileNotFoundError as e:
print("{}: {}".format(type(e).__name__, e))
except ValueError as e:
print("{}: {}".format(type(e).__name__, e))